To answer your questions, yes, I believe you are being taken advantage of.
And your baby is being over vaccinated, imo! (this is the most concerning, more so than just money grabbing vets) Pease check out these links on vaccinations protocols and more info so you can be informed about your Yorkies needs for vaccinations.
http://www.yorkietalk.com/forums/yor...-overview.html
I am so sorry and angry there are vets out there like this
Sorry you had to deal with this, and happy that you are questioning it, for your babys sake.
Unfortunately, finding a good vet is the same as finding a good human doc, you have to keep at it until you find one you are comfortable with and trust... not always easy, but critical IMO when choosing a doc for your Yorkie.
I would suggest you make a post in the regional forum section of YT and put out a call for good vet recommendations from Yorkie parents in your vicinity, then check them out, call them and ask if you can come in and meet the vets, assistants, etc. Then do some cost comparisons.
As for the check ups, seems excessive for sure (exam costs each time), too many shots, bordella that often is ridiculous and you have to decide if you even need it.
also, 700 seems very high for a neuter unless he has retained testicle(s), which makes it just as invasive as a spay, but still very high.